Substantial progress has been made over the last ten years in understanding how natural selection has driven the origin of species. However, we know little about the genetic basis of speciation - the genes that underlie the behavioral, morphological, and other traits that define the reproductive barriers between new species. Progress has been limited by a shortage of study systems that present both an understanding of ecological and evolutionary context and the requisite genomic resources. The young species pairs of threespine stickleback fish (Gasterosteus aculeatus complex) provide an outstanding opportunity to address fundamental questions concerning the genetics of species origin and persistence in nature. Coexisting 'limnetic' and 'benthic' species have evolved repeatedly in multiple small lakes and show parallel differences in many traits. Mating behaviors such as nesting habitat and mate preferences form the principal barrier to gene flow. Such behaviors are also contingent upon body size, shape, and ecological differences such as habitat, which therefore indirectly influence reproductive isolation. Survival and reproductive success of hybrids likewise depend on this suite of behavioral and morphological traits. The first aim of our proposed research is to investigate the genetic underpinnings of behaviors and morphological traits responsible for reproductive isolation between benthic and limnetic sticklebacks from two lakes (Priest and Paxton) using quantitative trait locus (QTL) mapping with high-density single nucleotide polymorphism (SNP) arrays. Second, we aim to determine whether behavioral traits causing reproductive isolation map to the same genomic regions as the morphological traits known to correlate with mate choice. Our third aim is to detect regions of the genome causing postzygotic isolation by measuring segregation distortion at SNP markers in these pond-raised hybrids compared with that in control embryos made in the laboratory. Finally, we will test whether the same genomic regions control species differences in behavior and morphology between two independently evolved species pairs (in Priest and Paxton Lakes). Importantly, these traits will be measured in controlled outdoor experimental ponds that mimic natural lake habitats and permit the expression of natural behaviors, diets, growth, and reproductive schedules. Since the stickleback has a fully sequenced genome and many other genetic tools available, the mapping experiments proposed here will be the first step in identifying genes that underlie reproductive isolation in natural stickleback populations. In addition, the results are likely to have important implications for understanding the genetic basis of behavioral variation and behavioral disorders in humans because many of the genetic and neural pathways that underlie behaviors are likely to be conserved between fish and humans. PUBLIC HEALTH RELEVANCE: Very little is known about the genes that influence the normal range of phenotypic variation seen in human behaviors and morphologies. Humans and sticklebacks have migrated and adapted to new environments over a similar evolutionary timeframe, and genetic and developmental pathways are conserved amongst vertebrates. Thus, sticklebacks provide an excellent vertebrate model system for studying the genetic architecture of phenotypic variation that has direct relevance to similar studies in humans.